Hi Pedro,

To add to Charl's response, the error with libpthread.so is an existing issue when NEST is installed using conda-forge: https://github.com/nest/nestml/issues/1256. 
Could you try installing NEST from source in the same mamba environment and try again? The installation instructions can be found here: https://nest-simulator.readthedocs.io/en/stable/installation/developer.html#dev-install

Hope this helps!

Regards,
Pooja

Dear Pedro,

Thank you for writing in! Let me address your questions one by one.

1 -- PyGSL is only an optional dependency; the warning can be safely ignored. I'm actually not sure where the PyGSL dependency comes from; it's not in the requirements.txt of ODE-toolbox, NESTML or NEST as far as I can see.

2 -- I think this is fine, but perhaps a conda/mamba expert can say more about this. (I am not a mamba user myself.)

3 -- The ``generate_target()`` function is the basic, primary function. The ``NESTCodeGeneratorUtils.generate_code_for()`` function is an additional convenience function, that will create temporary paths for the generated code, which is especially useful in a Jupyter notebook where the same cell (that invokes the code generation) may be run over and over again.

Hope this helps, please don't hesitate to get back in touch if you should run into any further issues or questions.

Yours,

Charl

On Wed, Feb 18, 2026, at 15:37, Pedro R. Pinheiro wrote:

Hi everyone. I have a couple of questions pertaining to NESTML and would appreciate some support.  I use NEST via WSL with Ubuntu 24.04.3 LTS. More specifically, I use the micromamba extension on VS Code to manage virtual environments and install python packages via conda-forge.

1) When using NEST 3.9 I get an error saying that PyGSL is incompatible and the simulator returns me a warning saying the stiffness test will be skipped.

WARNING:root:PyGSL is not available. The stiffness test will be skipped. WARNING:root:Error when importing: No module named 'pygsl  

I didn't have this problem before, when I used NEST 3.8. 

My installation steps currently are essentially:

micromamba install -c conda-forge nest-simulator=3.9 ipython cxx-compiler cmake make swig pkg-config

pip install nestml

When I try to install pygsl via micromamba the only version I can attempt is 2.6.2. Installing pygsl via pip also gives an error even if I have swig and pkg-config installed.

2) When generating a target using generate_target, I get the following error message:

/.micromamba/envs/default/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so: No such file or directory  

I realised that while I do not have libpthread.so under that path I do have libpthread.so.0 and creating a symlink directing the former to the latter solves the problem. Is this acceptable?

ln -s /.micromamba/envs/default/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so.0 /.micromamba/envs/default/x86_64-conda-linux-gnu/sysroot/usr/lib/libpthread.so

3) I would like to know if using NESTCodeGeneratorUtils.generate_code_for is better or equivalent to using generate_target.

That's it for now. Thank you in advance for your help.

Best,

Pedro.

_______________________________________________

NEST Users mailing list -- users@nest-simulator.org

To unsubscribe send an email to users-leave@nest-simulator.org

_______________________________________________
NEST Users mailing list -- users@nest-simulator.org
To unsubscribe send an email to users-leave@nest-simulator.org